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Concept

Microarray analysis techniques

Related publications (28)

Variability of Primary Sjogren's Syndrome Is Driven by Interferon alpha and Interferon alpha Blood Levels Are Associated With the Class II HLA-DQ Locus

Jacques Fellay, Christian Axel Wandall Thorball

Objective Primary Sjogren's syndrome (SS) is the second most frequent systemic autoimmune disease, affecting 0.1% of the general population. To characterize the molecular and clinical variabilities among patients with primary SS, we integrated transcriptom ...

WILEY2022

Confronting false discoveries in single-cell differential expression

Grégoire Courtine, Gioele La Manno, Quentin Barraud, Jordan Squair, Matthieu Pierre Gautier, Mark Andrew Anderson, Nicholas David James, Thomas Haynes Hutson, Claudia Kathe, Michael Alexander Skinnider, Rémi Bernard René Hudelle

Differential expression analysis of single-cell transcriptomics allows scientists to dissect cell-type-specific responses to biological perturbations. Here, the authors show that many commonly used methods are biased and can produce false discoveries. ...

Nature Portfolio2021

Common Gene Expression Patterns in Environmental Model Organisms Exposed to Engineered Nanomaterials: A Meta-Analysis

Kristin Schirmer

The use of omics is gaining importance in the field of nanoecotoxicology; an increasing number of studies are aiming to investigate the effects and modes of action of engineered nanomaterials (ENMs) in this way. However, a systematic synthesis of the outco ...

AMER CHEMICAL SOC2020

MicroRNA-204-5p modulates mitochondrial biogenesis in C2C12 myotubes and associates with oxidative capacity in humans

Xu Wang

Using an unbiased high-throughput microRNA (miRNA)-silencing screen combined with functional readouts for mitochondrial oxidative capacity in C2C12 myocytes, we previously identified 19 miRNAs as putative regulators of skeletal muscle mitochondrial metabol ...

2020

Label-free, scalable and point-of-care imaging platform for rapid analysis of biomarker

Hatice Altug, Filiz Yesilköy, Alexander Belushkin, Yasaman Jahani

We propose a disruptive point-of-care (PoC) imaging platform based on lens-free interference phase-contrast imaging for rapid detection of biomarker such as for sepsis and potentially other diseases (e.g. cancer). It enables simultaneous analysis of potent ...

SPIE-INT SOC OPTICAL ENGINEERING2019

Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data

Vassily Hatzimanikatis, Vikash Kumar Pandey

Nonalcoholic fatty liver disease (NAFLD) is associated with metabolic syndromes spanning a wide spectrum of diseases, from simple steatosis to the more complex nonalcoholic steatohepatitis. To identify the deregulation that occurs in metabolic processes at ...

2019

Phase-sensitive plasmonic biosensor using a portable and large field-of-view interferometric microarray imager

Hatice Altug, Filiz Yesilköy, Alexander Belushkin, Yasaman Jahani

Nanophotonics, and more specifically plasmonics, provides a rich toolbox for biomolecular sensing, since the engineered metasurfaces can enhance light–matter interactions to unprecedented levels. So far, biosensing associated with high-quality factor plasm ...

2018

Short-lived AUF1 p42-binding mRNAs of RANKL and BCL6 have two distinct instability elements each

Philipp Bucher, Giovanna Ambrosini, Lukas Kühn, Ramona Pauchard-Batschulat, Barbara Grisoni-Neupert

Regulation of mRNA stability by RNA-protein interactions contributes significantly to quantitative aspects of gene expression. We have identified potential mRNA targets of the AU-rich element binding protein AUF1. Myc-tagged AUF1 p42 was induced in mouse N ...

2018

Characterization of cancer stem cell subpopulations from patient-derived xenografts of advanced prostate cancer

Markus Germann

Androgen-deprivation therapy is the standard treatment for prostate cancer. Despite the initial response, a fraction of cases manifest progression to castration-resistant prostate cancer. PCa recurrence is possibly due to androgen-independent cancer stem c ...

AMER ASSOC CANCER RESEARCH2018

Mitochondria! function is impaired in the skeletal muscle of pre-frail elderly

Johan Auwerx, Pénélope Andreux

Aging is accompanied by a gradual decline in both muscle mass and strength over time, which can eventually lead to pathologies, such as frailty and sarcopenia. While these two conditions are well characterized, further investigation of the early biological ...

Nature Research2018

The gene family-free median of three

Background: The gene family-free framework for comparative genomics aims at providing methods for gene order analysis that do not require prior gene family assignment, but work directly on a sequence similarity graph. We study two problems related to the b ...

2017

The Gene Family-Free Median of Three

The gene family-free framework for comparative genomics aims at developing methods for gene order analysis that do not require prior gene family assignment, but work directly on a sequence similarity graph. We present a model for constructing a median of t ...

Springer AG2016

Comparative study of joint analysis of microarray gene expression data in survival prediction and risk assessment of breast cancer patients

Microarray gene expression data sets are jointly analyzed to increase statistical power. They could either be merged together or analyzed by meta-analysis. For a given ensemble of data sets, it cannot be foreseen which of these paradigms, merging or meta-a ...

Oxford Univ Press2016

Transcriptomic regulations in oligodendroglial and microglial cells related to brain damage following fetal growth restriction

Yohan Van de Looij, Maxime Olivier Baud

Fetal growth restriction (FGR) is a major complication of human pregnancy, frequently resulting from placental vascular diseases and prenatal malnutrition, and is associated with adverse neurocognitive outcomes throughout life. However, the mechanisms link ...

Wiley-Blackwell2016

Surface-initiated controlled radical polymerization enhanced DNA biosensing

Harm-Anton Klok, Tugba Bilgiç Tune

The surface chemistry at the DNA recognition and binding interface plays an important role in determining the performance of DNA microarrays and DNA biosensors. Surface-initiated controlled radical polymerization (SI-CRP) reactions represent a powerful too ...

2015

Abrogation of HMX1 Function Causes Rare Oculoauricular Syndrome Associated With Congenital Cataract, Anterior Segment Dysgenesis, and Retinal Dystrophy

PURPOSE. To define the phenotypic manifestation, confirm the genetic basis, and delineate the pathogenic mechanisms underlying an oculoauricular syndrome (OAS). METHODS. Two individuals from a consanguineous family underwent comprehensive clinical phenotyp ...

Assoc Research Vision Ophthalmology Inc2015

The Phosphoinositide 3-Kinase p110 alpha Isoform Regulates Leukemia Inhibitory Factor Receptor Expression via c-Myc and miR-125b to Promote Cell Proliferation in Medulloblastoma

Medulloblastoma (MB) is the most common malignant brain tumor in childhood and represents the main cause of cancer-related death in this age group. The phosphoinositide 3-kinase (PI3K) pathway has been shown to play an important role in the regulation of m ...

Public Library of Science2015

Deciphering the astrocyte-neuron metabolic cooperation in vivo

Manuel Raphael Zenger

Brain energy consumption is high and a very tightly regulated energy metabolism ensures correct performance. Neurons, the cells responsible for transmitting information via synapses, interact very closely with star shaped glial cells called astrocytes. Ast ...

EPFL2015

Meta-analysis of Incomplete Microarray Studies

Alix Corinne Josiane Colette Zollinger

Meta-analysis of microarray studies to produce an overall gene list is relatively straightforward when complete data are available. When some studies lack information, providing only a ranked list of genes, for example, it is common to reduce all studies t ...

EPFL2014

Novel ADAM9 homozygous mutation in a consanguineous Egyptian family with severe cone-rod dystrophy and cataract

Tatiana Favez

Objective To genetically and phenotypically describe a new ADAM9 homozygous mutation in a consanguineous family from Egypt with autosomal recessive cone-rod dystrophy (arCRD), anterior polar and posterior subcapsular cataract. Design, setting and participa ...

Bmj Publishing Group2014